I've been swimming with my Apple watch series 2 for a few months. I normally swim about 50-60 lengths of the pool with mixed strokes about 2-3 times a week. Okay, on my first swim I noticed some discrepancies, as well, and it's not until I swam a few more times, that I understood a little more how it counts lap. I hope some of this info will help you...
1. As I believe it was briefly mentioned at the announce of the Series 2, the watch runs some internal algorithms to calibrate your stroke to distance. At least in my case, once I swam a few times, it did appear to dial in to counting my laps more accurately.
2. If you are mixing strokes, the algorithms that count laps may need a bit more time to accurately count your different strokes. For example, in my case, I only swim a limited amount of back stroke, and breast stroke, so it took a few swims to dial these in.
3. The lap counting, at least for me, is highly dependent on a "nice even stroke". Depending on how much swimming you do, if your stroke gets lazy, as it does for me, it can get off by a few feet on some laps of the pool. If your not a regular swimmer, with a nice even stroke, I think this could be a larger issue.
4. I also perform "kick boarding" as part of my swimming exercise. Of course with "kick boarding" you don't typically swing your arms, so the watch won't pick this up in any accurate way. However, when I go into the turns with the kick board, sometimes my arms flap around a little, so sometimes it throws a few yards into my total swim. No big deal, I would love to be able to "manually" add these laps, but as you've noticed, it can't be done.
5. I often perform interval swimming, so I take a short break between some fixed number laps for heart rate recovery. I've found that if I tap the watch face just after touching the wall, and coming up for some air, it may not have credited me for the "last lap". I've found that it's just on the edge of counting the lap, so all it takes is a small swing of the arm for the lap count to increment. I think the watch actually goes into a "wait and see" moment, since it's not sure what your doing in the pool, it seems like it will eventually count the lap, if you lie idle for a couple of minutes.
6. If your a regular at flip-turns, I think it's normally dead on for counting laps, at least that's been my experience for freestyle. If you don't flip-turn then I would just say that it's probably just a good idea to develop a pretty regular turning style, and I'll have to assume the watch will properly pick this up, and better calibrate your stroke to the pool distance.
In general, I've been incredibly pleased with the accuracy, so I hope others see the same. There have been a few times, it's been off by half a lap, but I normally attribute it to my "stroke" falling off and getting lazy, or possibly I stopped for a minute to adjust my goggles, or speak with the person I'm sharing the lane, or my turns weren't very consistent. I think these throw things off a bit, but that's just my experience.
Good luck...
